rs7758893

Variant names:

• chr6-89206922-C-T
• rs7758893
• NM_002042.5:c.123-3437G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002042.5(GABRR1):​c.123-3437G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,118 control chromosomes in the GnomAD database, including 49,703 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (49703 hom., cov: 32)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 6 publications found

Genes affected

GABRR1 (HGNC:4090): (gamma-aminobutyric acid type A receptor subunit rho1) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. GABRR1 is a member of the rho subunit family. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.123-3437G>A		intron_variant	Intron 1 of 9	ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.123-3437G>A		intron_variant	Intron 1 of 9	1	NM_002042.5	ENSP00000412673.2

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121684 AN: 152000 Hom.: 49650 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.794

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.801 AC: 121797 AN: 152118 Hom.: 49703 Cov.: 32 AF XY: 0.788 AC XY: 58589 AN XY: 74350

African (AFR) AF: 0.905 AC: 37610 AN: 41540

American (AMR) AF: 0.713 AC: 10892 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3069 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1841 AN: 5138

South Asian (SAS) AF: 0.763 AC: 3676 AN: 4816

European-Finnish (FIN) AF: 0.667 AC: 7042 AN: 10554

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55049 AN: 68000

Other (OTH) AF: 0.793 AC: 1675 AN: 2112

Alfa AF: 0.806 Hom.: 80152

Bravo AF: 0.808

Asia WGS AF: 0.592 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7758893; hg19: chr6-89916641; COSMIC: COSV65620841;